Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.)

doi:10.1111/j.1365-313X.2007.03244.x

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Wiley InterScience

The Plant Journal

Volume 52 Issue 3, Pages 391 - 404

Published Online: 30 Aug 2007

Published in association with the Society for Experimental Biology

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Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.)

Kazuhiro Ohtsu ¹ , Marianne B. Smith ¹ , Scott J. Emrich ² , Lisa A. Borsuk ² , Ruilian Zhou ¹ , Tianle Chen ³ , Xiaolan Zhang ³ , Marja C. P. Timmermans ⁴ , Jon Beck ⁵ , Brent Buckner ⁶ , Diane Janick-Buckner ⁶ , Dan Nettleton ^2,7,8 , Michael J. Scanlon ^3,9 and Patrick S. Schnable ^1,2,8,*

¹ Department of Agronomy, Iowa State University, Ames, IA 50011, USA,
² Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA 50011, USA,
³ Plant Biology Department, University of Georgia, Athens, GA 30602, USA,
⁴ Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA,
⁵ Division of Mathematics and Computer Science, Truman State University, Kirksville, MO 63501, USA,
⁶ Division of Science, Truman State University, Kirksville, MO 63501, USA,
⁷ Department of Statistics, Iowa State University, Ames, IA 50011, USA,
⁸ Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA, and
⁹ Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA

Correspondence to *(fax +1 515 294 5256; e-mail schnable@iastate.edu).

KEYWORDS

shoot apical meristem • global gene expression • laser capture microdissection • 454 sequencing • development • retrotransposon expression

ABSTRACT

All above-ground plant organs are derived from shoot apical meristems (SAMs). Global analyses of gene expression were conducted on maize (Zea mays L.) SAMs to identify genes preferentially expressed in the SAM. The SAMs were collected from 14-day-old B73 seedlings via laser capture microdissection (LCM). The RNA samples extracted from LCM-collected SAMs and from seedlings were hybridized to microarrays spotted with 37 660 maize cDNAs. Approximately 30% (10 816) of these cDNAs were prepared as part of this study from manually dissected B73 maize apices. Over 5000 expressed sequence tags (ESTs) (about 13% of the total) were differentially expressed (P < 0.0001) between SAMs and seedlings. Of these, 2783 and 2248 ESTs were up- and down-regulated in the SAM, respectively. The expression in the SAM of several of the differentially expressed ESTs was validated via quantitative RT-PCR and/or in situ hybridization. The up-regulated ESTs included many regulatory genes including transcription factors, chromatin remodeling factors and components of the gene-silencing machinery, as well as about 900 genes with unknown functions. Surprisingly, transcripts that hybridized to 62 retrotransposon-related cDNAs were also substantially up-regulated in the SAM. Complementary DNAs derived from the LCM-collected SAMs were sequenced to identify additional genes that are expressed in the SAM. This generated around 550 000 ESTs (454-SAM ESTs) from two genotypes. Consistent with the microarray results, approximately 14% of the 454-SAM ESTs from B73 were retrotransposon-related. Possible roles of genes that are preferentially expressed in the SAM are discussed.

Received 8 May 2007; accepted 31 May 2007.

DIGITAL OBJECT IDENTIFIER (DOI)

10.1111/j.1365-313X.2007.03244.x About DOI